Detected Missense Mutations Research Articles

TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants.

Wilms tumors (WTs) are histologically diverse childhood cancers with variable contributions of blastema, stroma, and epithelia. A variety of cancer genes operate in WTs, including the tripartite-motif-containing-28 gene (TRIM28). Case reports and small case series suggest that TRIM28 mutations are associated with epithelial morphology and WT predisposition. Here, we systematically investigated the prevalence of TRIM28 inactivation and predisposing mutations in a cohort of 126 WTs with >2/3 epithelial cells, spanning 20 years of biobanking in the German SIOP93-01/GPOH and SIOP2001/GPOH studies. Overall, 44.4% (56/126) cases exhibited loss of TRIM28 by immunohistochemical staining. Of these, 48 could be further analyzed molecularly, revealing TRIM28 sequence variants in each case - either homozygous (~2/3) or heterozygous with epigenetic silencing of the second allele (~1/3). The majority (80%) of the mutations resulted in premature stops and frameshifts. In addition, we detected missense mutations and small deletions predicted to destabilize the protein through interference with folding of key structural elements such as the zinc-binding clusters of the RING, B-box-2, and PHD domains or the central coiled-coil region. TRIM28-mutant tumors otherwise lacked WT-typical IGF2 alterations or driver events, except for rare TP53 progression events that occurred with expected frequency. Expression profiling identified TRIM28-mutant tumors as a homogeneous subset of epithelial WTs that mostly present with stage I disease. There was a high prevalence of perilobar nephrogenic rests, putative precursor lesions, that carried the same biallelic TRIM28 alterations in 7/7 cases tested. Importantly, 46% of the TRIM28 mutations were present in blood cells or normal kidney tissue, suggesting germline events or somatic mosaicism, partly supported by family history. Given the high prevalence of predisposing variants in TRIM28-driven WT, we suggest that immunohistochemical testing of TRIM28 be integrated into diagnostic practice as the management of WT in predisposed children differs from that with sporadic tumors. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

АНАЛИЗ ПАТОГЕННОСТИ НОВОЙ МИССЕНС-МУТАЦИИ В ГЕНЕ MYOF, ВЫЯВЛЕННОЙ У ПАЦИЕНТКИ С НАСЛЕДСТВЕННЫМ АНГИООТЕКОМ С НОРМАЛЬНЫМ УРОВНЕМ C1-ИНГИБИТОРА

Hereditary angioedema (HAE) is a genetically determined disorder accompanied by specific symptoms associated with sporadic subcutaneous and submucosal edema. The described cases of type III HAE not associated with mutations in the SERPING1 gene are characterized by the corresponding clinical picture with normal values and functional activity of the C1-inhibitor. Type III HAE is associated with mutations in the F12, PLG, ANGPT1, KNG1, MYOF, and HS3ST6 genes. Mutations in the MYOF and HS3ST6 genes remain the least studied as yet. And as for the MYOF gene, a single mutation, Arg217Ser, is known to be associated with the development of HAE. The purposes of this research were to study the new missense mutation NC_000010.10:g.95093020C>T in the MYOF gene and predictive assessment of its contribution to the HAE pathogenesis using the bioinformatics analysis. There was a blood sample obtained from a 14 y/o female patient with HAE clinical manifestations and without a decrease in the level and the lack in function of the C1-inhibitor. The research methods included sequencing of the patient's complete exome, bioinformatic analysis of the MYOF gene mutation using a number of databases and Internet resources with the purpose of assessing the conservation of the amino acid position of the substitution and predicting the effect of the mutation on the protein. Results: the girl had a previously undescribed missense mutation NC_000010.10:g.95093020C>T in exon 42 of the MYOF gene (isoform A) in the heterozygous state. The mutation resulted in the replacement of arginine with glutamine at position 1590 of the amino acid sequence (p.Arg1590Gln, rs201619869). The use of bioinformatics analysis allowed assuming the potential pathogenicity of the detected missense mutation, which could cause the observed edema. The possible pathways for the involvement of myoferlin with the detected mutation in the HAE pathogenesis are discussed in the Article. The use of in silico analysis allowed conducting the detailed study of the detected mutation considering its effect on the protein structure, which is the basis of its normal functioning. According to the results of the study, rare mutations in the MYOF gene can be involved in the HAE pathogenesis provoking edema through various cascades of biochemical reactions. In the course of the study, a new missense mutation in the MYOF gene, pathogenetically significant for the HAE development, was described for the first time.

Abstract 1907: Unique and novel deleterious MSH6 mutation among African American patients with colorectal cancer

Abstract Background: Colorectal cancer (CRC) incidence and mortality in African Americans (AA) is higher compared to Caucasians (CAU). It has also been reported that the disparity is due to differences in the mutation spectrum particularly germline mutations in the DNA mismatch repair (MMR) genes (such as hMSH6). Aim: We aimed to determine MSH6 mutation profile in AAs with CRC. Methods: We performed RNA sequencing in 8 paired CRC samples (AA, n=4 and CAU, n=4) to identify the unique transcript and novel pathogenic mutation in AA compared to CAU by comparing CRC matched to corresponding normal epithelia. In silico analysis of TCGA COAD RNA sequencing data was performed. Results: We found non-synonymous germline mutations (p.G1139S) in exon 5 of MSH6 gene (one of the MMR genes) in AA CRC samples. Interestingly, this mutation is present in the active site of ATP binding (1135 to 11442 residue) motif of MSH6 protein. In silico analysis was used to determine the novelty and pathogenicity of this mutation by comparison to various publicly available databases. Also, the deleterious effect of p.G1139S missense mutation on the structure of MSH6 protein revealed that p.G1139S is destabilizing MSH6 protein. Based on Ramachandran plot analysis, we found lot of clash and outliers in the mutant type compared to wild type MSH6 protein. Structural analysis revealed that serine substitution results in a wide ATP binding site compared to glycine present in wild-type MSH6. In addition, we found a loss of hydrogen bonding or gain of ionic interaction between wild-type and mutant MSH6 protein. Conclusion: Based on our in silico analysis, the deleterious effect of the detected missense mutation in the active site of ATP binding motif of MSH6 affects the structure and function of MSH6. This may result in the accumulation of mono-, or di-nucleotide repeats instability in the genome, leading to genomic alterations that associate with carcinogenesis in African American CRC patients. Citation Format: Mudasir Rashid, Rumaisa Rashid, Sudhir Varma, Zaki Sherif, John Carethers, Hassan Brim, Hassan Ashktorab. Unique and novel deleterious MSH6 mutation among African American patients with colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1907.

Rare deleterious mutations in Bruton’s tyrosine kinase as biomarkers for ibrutinib-based therapy: an in silico insight

Squamous cell carcinoma (SCC) is the second most common type of skin cancer caused by malignant keratinocytes. Multiple studies have shown that protein mutations have a significant impact on the development and progression of cancer, including SCC. We attempted to decode the effect of single amino acid mutations in the Bruton's tyrosine kinase (BTK) protein in this study. Molecular dynamic (MD) simulations were performed on selected deleterious mutations of the BTK protein, revealing that the variants adversely affect the protein, indicating that they may contribute to the prognosis of SCC by making the protein unstable. Then, we investigated the interaction between the protein and its mutants with ibrutinib, a drug designed to treat SCC. Even though the mutations have deleterious effects on protein structure, they bind to ibrutinib similarly to their wild type counterpart. This study demonstrates that the effect of detected missense mutations is unfavorable and can result in function loss, which is severe for SCC, but that ibrutinib-based therapy can still be effective on them, and the mutations can be used as biomarkers for Ibrutinib-based treatment. Seven different computational techniques were used to compute the effect of SAVs in accordance with the experimental requirements of this study. To understand the differences in protein and mutant dynamics, MD simulation and trajectory analysis, including RMSD, RMSF, PCA, and contact analysis, were performed. The free binding energy and its decomposition for each protein-drug complex were determined using docking, MM-GBSA, MM-PBSA, and interaction analysis (wild and mutants).

Structural and functional characterization of SARS-CoV-2 nucleocapsid protein mutations identified in Turkey by using in silico approaches

Missense mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus may cause changes in the structure of proteins. The nucleocapsid (N) protein is an important target for drugs and vaccines. The main purpose of this study is to detect missense mutations in the SARS-CoV-2 Nprotein and to reveal the effects of these mutations on protein structure by using in silico approaches. 161 missense mutations of the Nprotein were determined in 2286 SARS-CoV-2 genomes derived from the GISAID EpiCoV database in the Turkish population. Identified 161 missense mutations were analyzed by using sequence and structure-based methods to predict effects of mutation on function and structure of SARS-CoV-2 Nprotein. These analyzes revealed that some mutations showed deleterious effects and change of stability and flexibility of nucleocapsid protein. D3L, S194L, S235F, and P13L (Omicron variant) mutations were further analyzed in our study due to their importance in the literature and in our results. Even though, our findings are essential for research of SARS-CoV-2 virus, in vitro and in vivo validations are necessary. Keywords: nucleocapsid protein; SARS-CoV-2; missense mutations; protein stability; protein flexibility.

Alternations in mitochondrial genome in carcinogenesis of HPV positive cervix

ObjectiveIt is well known that mitochondrial dysfunctions are involved in tumorigenesis. A special interest of scientists is mitochondrial ND1 gene (mtND1). Recently detected mutations in the mtND1 can disrupt the normal activity of complex I and affect oxidative phosphorylation, thus leading to increase reactive oxygen species production. This study was undertaken to determine the alternations in the mtND1 and evaluate their association with development of precancerous lesions and cervical cancer. MethodsIn the study 29 cervical cancer, 28 low grade squamous intraepithelial lesion (L-SIL) and 30 high grade squamous intraepithelial lesion (H-SIL) HPV positive fragments tissue were screened for the presence of mtND1 mutations. ResultsOur study showed that mutations in the mtND1 gene were detected in patients with precancerous stage, as well as cervical cancer. We have identified 12 point mutations in 116 analyzed precancerous and cancer samples HPV positive. Most detected missense mutations were previously described, except one (p. M156K) with Grantham value 95. The lower expression of mRNA ND1 was detected in cervical cancer cases and in all samples in which mtND1 mutations were identified. Our analyses revealed that level of ROS production was higher in cervical cancer tissues and all cases characterized by mtND1 mutations. ConclusionsWe hypothesize that mutations in MT-ND1 observed in H-SIL and cancer could activate cervical carcinogenesis by increased ROS production.

In Silico Approach for Prediction of the Structural and Functional Impacts of 184(T>C) Missense Mutation Identified in BRCA1 Gene in a Syrian Breast Cancer Patient

Background: The classification of genetic variations depending on their clinical impacts is highly relevant for clinical decision-making. Therefore, predicting the effects of missense mutations using in silico tools has become a frequently employed approach. The objective of this study was to analyze the impacts of a previously detected BRCA1 missense mutation using an in silico prediction tool in the context of invasive breast cancer. Methods: In this bioinformatics study, application of the in silico combination of tools Phyre2 to 184(T>C), a BRCA1 missense mutation previously characterized by Khalil et al. in 2018, we used to predict its clinical impacts. Results: Incidence of the missense mutation caused a disorder in the zinc binding RING finger functional domain of BRCA1 protein. This incidence was considered to be a major contributor to the interaction of this protein with other proteins in signal transduction pathway in the mechanism of cellular response to DNA damage. The functional analysis also revealed that the detected missense mutation might significantly affect the function of both the protein and phenotype of the living organism. Conclusion: In silico prediction confirmed the detrimental impact of the identified missense mutation in the exon 2 of BRCA1 gene on both the structural and functional properties of the generated BRCA1 protein.

Monitoring of cancer patients via next-generation sequencing of patient-derived circulating tumor cells and tumor DNA.

Liquid biopsy of circulating tumor cells (CTC) and circulating tumor DNA (ctDNA) is gaining attention as a method for real‐time monitoring in cancer patients. Conventional methods based upon epithelial cell adhesion molecule (EpCAM) expression have a risk of missing the most aggressive CTC subpopulations due to epithelial‐mesenchymal transition and may, thus, underestimate the total number of actual CTC present in the bloodstream. Techniques utilizing a label‐free inertial microfluidics approach (LFIMA) enable efficient capture of CTC without the need for EpCAM expression. In this study, we optimized a method for analyzing genetic alterations using next‐generation sequencing (NGS) of extracted ctDNA and CTC enriched using an LFIMA as a first‐phase examination of 30 patients with head and neck cancer, esophageal cancer, gastric cancer and colorectal cancer (CRC). Seven patients with advanced CRC were enrolled in the second‐phase examination to monitor the emergence of alterations occurring during treatment with epidermal growth factor receptor (EGFR)‐specific antibodies. Using LFIMA, we effectively captured CTC (median number of CTC, 14.5 cells/mL) from several types of cancer and detected missense mutations via NGS of CTC and ctDNA. We also detected time‐dependent genetic alterations that appeared during anti–EGFR therapy in CTC and ctDNA from CRC patients. The results of NGS analyses indicated that alterations in the genomic profile revealed by the liquid biopsy could be expanded by using a combination of assays with CTC and ctDNA. The study was registered with the University Hospital Medical Information Network Clinical Trials Registry (ID: UMIN000014095).

PF335 MUTATION SPECTRUM OF F8 GENE IN HEMOPHILIA A PATIENTS FROM RUSSIA

Background:Congenital hemophilia A (HA) is an inherited recessive X‐linked bleeding disorder caused by a wide spectrum of mutations in the F8 gene and affected 1 in 5000 males. Its high degree of mutational heterogeneity complicates the carrier and prenatal diagnoses for genetic counseling but offers a wealth of data on the relationship between structure and function of FVIII.Aims:The aim of this study was to describe mutation spectrum in Russian patients with HA and to improve significantly genetic carriage and prenatal diagnostics of this disease in our country. Study results are especially important for families with sporadic form of HA (i.e. in families with the first reported patient), because in these cases only genetic analysis can give a reliable carriage status for proband's mothers.Methods:We conducted molecular genetic analysis for 239 unrelated patients with different forms of HA, recruited from 1990 to 2019 from different regions of Russia. Genomic DNA was isolated from peripheral blood using phenol–chloroform extraction. All patients with severe HA were examined for intron 22 (LD‐PCR method, modified from Liu et al., 1998 and Bagnall et al, 2006) and intron 1 (Bagnall et al., 2002) inversions. For patients without inversions we sequenced all functionally significant F8 gene fragments by Sanger.Results:We found inversion 22 in 130 unrelated patients with severe hemophilia A (68%, 17 patients with inhibitor). In 11 patients we found inversion 1 (5.8%, 1 patient with inhibitor), 3 patients had abnormal inversion 1 with additional deletion or duplication of nearby regions. In other 98 patients we detected 79 different mutations (12 patients with inhibitor), 40 of which had never been reported before in the international databases. Among them prevailed missense mutations (37), there were also nonsense (15), frameshift (13, 3 of them were indels), splicing mutations (9), large deletions (4) and inframe deletion (1). In three patients we found two mutations simultaneously. Five patients were women suffered from HA. One of them carried two mutations in F8 gene, others had only one mutation (one carried a missense mutation, while others had inversion 22), but we found for them evidence for an asymmetric inactivation of X‐chromosome using HUMARA test.Summary/Conclusion:All mutations detected in this study were distributed uniformly along the FVIII gene. As expected, significant part of missense and nonsense mutations occurred in CpG hot spot dinucleotides (21 out 52). We found two other mutation hot spots located in oligoA tracts of exon 14: p.Asn1460Lysfs∗1 and p.Ile1213Phefs∗5 detected in four and six unrelated patients, respectively. During our work we revealed a new mutation p.His634Arg found in 7 patients with mild HA (F8 = 10–30%) originated from Sverdlovsk region of Russia. We constructed four‐loci haplotypes for those patients and for 10 other patients with HA from the same region carrying other different mutations. All patients with this mutation shared the same unique haplotype, while all other patients had different haplotypes, which indicates founder effect for p.His634Arg substitution. For two large deletions (del Ex6 and del Ex6–12) we determined breakpoints, which were in both cases located within or nearby Alu‐repeats. In our cases HA in women mostly developed as a result of an asymmetric inactivation of X‐chromosome. For one woman with this inactivation we detected missense mutation led to a late manifestation of the disease (at 59 years old), which was at first diagnosed as acquired HA.

New variants in COL5A1 gene among Polish patients with Ehlers-Danlos syndrome: analysis of nine cases.

IntroductionThe Ehlers-Danlos syndrome (EDS) is a non-inflammatory, heritable connective tissue disorder divided into 13 types according to the 2017 International Classification of the Ehlers-Danlos syndromes. One of the subtypes of EDS, classical (cEDS), is characterized by joint hypermobility, skin hyperextensibility and atrophic scars, which are major criteria of cEDS.AimIn this study, the first in Central Eastern Europe, 44 patients were investigated. All of them were tested for COL5A1 mutations with direct DNA sequencing.Material and methodsThe study group included 44 patients of Polish origin, all of whom fulfilled criteria for the classical type of Ehlers-Danlos syndrome. Direct sequencing of the COL5A1, COL5A2 and COL1A1 c.934C>T genes was performed for all of them. Evaluation of potential pathogenicity of detected missense mutation was conducted using SIFT (Sorting Intolerant from Tolerant), PolyPhen-2, AlignGVGD (Align Grantham Variance/Grantham Difference). The effect of the splice site mutations was predicted by Human Splicing Finder and NetGene2 tools.ResultsAmong all tested patients, nine mutations of COL5A1 gene were detected (8 missense mutations and 1 splice site). The alterations identified by us are new, hitherto not described in other reports. Evaluation of the mutations by in silico tools indicate their pathogenicity.ConclusionsOur study is the first COL5A1 gene molecular investigation conducted among cEDS patients from Central Eastern Europe. Besides new COL5A1 variant findings, we gained molecular confirmation of clinical diagnosis of cEDS. In some cases, specific and adequate evaluation and classification of EDS patients based only on clinical features, may be difficult.

Multi-azole-resistant strain of Malassezia pachydermatis isolated from a canine Malassezia dermatitis

In the case presented here, we describe the isolation of an azole-resistant strain of M. pachydermatis from a canine Malassezia dermatitis. The isolate (NUBS18001) from this case exhibited a minimum inhibitory concentration (MIC) of 320μg/ml to itraconazole (ITZ) by broth microdilution (BM) assay, >32μg/ml to ITZ by E-test, and >32μg/ml to KTZ by E-test. Synergistic effects between FK506 and ITZ in the azole-resistant strain was evaluated using the microdilution checker-board method. The ITZ-resistant strain exhibited MICs of 320μg/mL of ITZ alone and 5μg/ml of FK506 alone; the addition of FK506 attenuated the ITZ MIC to 2.5μg/ml, yielding an ITZ FICI value of 0.507. This result suggested that the combination of ITZ and FK506 exerted an additive effect against the ITZ-resistant strain. To understand the other mechanism inferred to be present in our multi-azole-resistant strain, we sequenced the ERG11 gene from this isolate, and detected missense mutations (A412G and C905T) in the sequence of the ERG11 open reading frame (ORF). To the best of our knowledge, this work is the first report that a multi-azole-resistant M. pacydermatis strain contains mutations in ERG11.

Genetic causes of deaf‐blindness in sixteen Czech families

PurposeUsher syndrome (USH) is the most common cause of hereditary deaf‐blindness in humans with an estimated prevalence of 3‐6 per 100,000 inhabitants. USH is inherited as an autosomal recessive trait and is clinically divided into three types based on audiological profile and vestibular symptoms. The aim of the project was to phenotype the first cohort of Czech patients with USH (16 families, 21 affected individuals) and to perform investigation into the molecular genetic cause of their disease.MethodsSanger sequencing of 6 frequently mutated USH2A exons was performed as an initial step in probands suspected to suffer from USH type II. Unsolved cases were then investigated by a range of techniques including whole‐exome sequencing, targeted gene panel next generation sequencing and single‐nucleotide polymorphism (SNP) array for copy number variation analysis. Detected missense mutations were evaluated for pathogenicity by six in silico tools. Mutations were verified and their segregation within the families was performed by Sanger sequencing.ResultsIn total 17 different mutations evaluated as pathogenic were identified in 20 individuals (95%) from 15 families, of these c.1256G>A, c.13342_13347del, deletion of exons 33 and 34 in USH2A, c.871G>A in CDH23 and c.937C>T in USH1C were novel. A known c.11864G>A in USH2A was the most prevalent mutation observed, found either in a homozygous or compound heterozygous state in 9 families. SNP haplotype analysis supported the hypothesis of a founder effect. Investigation into the geographic origin suggested regional clustering of the c.11864G>A allele in Southeastern part of the Czech Republic.ConclusionsThe proposed research will help to elucidate factors involved in the etiopathogenesis of USH, which is important for prognosis, patient counseling, management, development and introduction of novel therapies.

Mutation spectrum of the FZD-4, TSPAN12 AND ZNF408 genes in Indian FEVR patients.

BackgroundMutations in candidate genes that encode for a ligand (NDP) and receptor complex (FZD4, LRP5 and TSPAN12) in the Norrin β-catenin signaling pathway are involved in the pathogenesis of familial exudative vitreoretinopathy (FEVR, MIM # 133780). Recently, a transcription factor (ZNF408) has also been implicated in FEVR. We had earlier characterized the variations in NDP among FEVR patients from India. The present study aimed at understanding the involvement of the remaining genes (FZD4, TSPAN12 and ZNF408) in the same cohort.MethodsThe DNA of 110 unrelated FEVR patients and 115 unaffected controls were screened for variations in the entire coding and untranslated regions of these 3 genes by resequencing. Segregation of the disease-associated variants was assessed in the family members of the probands. The effect of the observed missense changes were further analyzed by SIFT and PolyPhen-2 scores.ResultsThe screening of FZD4, TSPAN12 and ZNF408 genes identified 11 different mutations in 15/110 FEVR probands. Of the 11 identified mutations, 6 mutations were novel. The detected missense mutations were mainly located in the domains which are functionally crucial for the formation of ligand-receptor complex and as they replaced evolutionarily highly conserved amino acids with a SIFT score < 0.005, they are predicted to be pathogenic. Additionally 2 novel and 16 reported single nucleotide polymorphisms (SNP) were also detected.ConclusionsOur genetic screening revealed varying mutation frequencies in the FZD4 (8.0 %), TSPAN12 (5.4 %) and ZNF408 (2.7 %) genes among the FEVR patients, indicating their potential role in the disease pathogenesis. The observed mutations segregated with the disease phenotype and exhibited variable expressivity. The mutations in FZD4 and TSPAN12 were involved in autosomal dominant and autosomal recessive families and further validates the involvement of these gene in FEVR development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12886-016-0236-y) contains supplementary material, which is available to authorized users.

Identification of Genetic Polymorphisms of CYP2W1 in the Three Main Chinese Ethnicities: Han, Tibetan, and Uighur.

CYP2W1 is an orphan member of the cytochrome P450 superfamily. Recently, CYP2W1 has gained great research interest because of its unknown enzymatic function and tumor-specific expression property. This study aims to investigate the genetic polymorphisms of the CYP2W1 gene in Chinese populations and explore the functions of the detected variants. All of the nine exons and exon-intron junction regions of the CYP2W1 gene were sequenced in 150 Chinese subjects, including 50 Han Chinese, 50 Tibetans, and 50 Uighurs. A total of 26 genetic variants were identified in this study, and 19 polymorphisms were detected in each population. Frequency comparison between populations showed that nine variants exhibited significantly different allelic distributions. A total of 12 different haplotypes were inferred from 150 samples by using the genotype data of nine exonic variants found in this study. CYP2W1*1A, *1B, *2, *4, and *6 were detected as the main alleles/haplotypes. Moreover, one, three, and two ethnically specific haplotypes were observed in the Han, Tibetan, and Uighur samples, respectively. Then, the effects of four detected missense mutations (Ala181Thr, Gly376Ser, Val432Ile, and Pro488Leu) on the CYP2W1 protein function were predicted using three in silico tools: Polymorphism Phenotyping v2, Sorts Intolerant from Tolerant, and MutationTaster. The results showed that Gly376Ser and Pro488Leu may have deleterious effects. In summary, this study showed that the genetic pattern of CYP2W1 is interethnically different among the three Chinese populations, and this finding can extend our understanding of population genetics of CYP2W1 in the Chinese population.

Classification and Tie2 mutations in spinal and soft tissue vascular anomalies

Vascular anomalies included hemangiomas and vascular malformations (VMs). VMs are mediated by mutations in the endothelial cell-specific receptor tyrosine kinase Tie2 (TEK),which is essential for angiogenesis and vascular stabilization. We identified five types of Tie2 mutations in 80 patients with soft tissue or spinal VMs by PCR including the previously detected missense mutations 2690A>G (Y897C), 2740C>T (L914F), 2743C>T (R915C), and two nonsense mutations 2763G>A, 2688C>T, we identified Tie2 mutation in primary spinal VMs for the first time. Tie2 mutations were found to be absent in 33 patients with hemangiomas and DNA samples of VMs. In addition, we showed that Tie2 mRNA expression in spinal VMs was similar to soft tissue VMs, but obviously lower than infant hemangiomas (P<0.01). This study provides new insights into spinal VMs, the association of Tie2 and vascular anomalies needs to be further discussed.

Molecular determination of glutaric aciduria type I in individuals from southwest Iran.

Glutaric Aciduria type 1 (GA1) is a metabolic inborn error and is characterized by increasing excursion of glutaric acid and its derivates, presented in microcephaly and dystonia. The disease is resulted from mutational inactivation in the GCDH gene encoding the glutaryl-CoA dehydrogenase. The defective enzyme causes the accumulation of an excessive level of intermediate breakdown products that leads to the brain damage. In spite of the clinical features, diagnosis of GAI has been often confusing, because of variability in the clinical manifestations of patients. Early diagnosis and treatment can though prevent irreversible disease progression and consequent brain damage; otherwise the affected individuals will die in their first decade of lives. The GCDH gene was also analyzed to (detect or identify) disease causing mutations using gene amplification and direct sequencing in 18 patients. Among 18 patients, 10 patients (55.5%) were homozygous or compounded heterozygous for the recurrent mutation E181Q, three patients (16.7%) were homozygous for the known mutation R402Q and one patient (5.6%) was compound heterozygous for S255L. All three detected missense mutations are pathogenic, which cause structural changes in the binding site and tetramerization or functional deficiency. Four other individuals (22.2%) with a preliminary diagnosis of GAI were negative for any pathogenic mutations. Most GA1 affected persons in southwest Iran are with Persian ethnicity and the most common mutation in Khuzestan Province is prominent in comparison to previous reports from Iran.

CLCN1 Mutations in Czech Patients with Myotonia Congenita, In Silico Analysis of Novel and Known Mutations in the Human Dimeric Skeletal Muscle Chloride Channel

Myotonia congenita (MC) is a genetic disease caused by mutations in the skeletal muscle chloride channel gene (CLCN1) encoding the skeletal muscle chloride channel (ClC-1). Mutations of CLCN1 result in either autosomal dominant MC (Thomsen disease) or autosomal recessive MC (Becker disease). The ClC-1 protein is a homodimer with a separate ion pore within each monomer. Mutations causing recessive myotonia most likely affect properties of only the mutant monomer in the heterodimer, leaving the wild type monomer unaffected, while mutations causing dominant myotonia affect properties of both subunits in the heterodimer. Our study addresses two points: 1) molecular genetic diagnostics of MC by analysis of the CLCN1 gene and 2) structural analysis of mutations in the homology model of the human dimeric ClC-1 protein. In the first part, 34 different types of CLCN1 mutations were identified in 51 MC probands (14 mutations were new). In the second part, on the basis of the homology model we identified the amino acids which forming the dimer interface and those which form the Cl- ion pathway. In the literature, we searched for mutations of these amino acids for which functional analyses were performed to assess the correlation between localisation of a mutation and occurrence of a dominant-negative effect (corresponding to dominant MC). This revealed that both types of mutations, with and without a dominant-negative effect, are localised at the dimer interface while solely mutations without a dominant-negative effect occur inside the chloride channel. This work is complemented by structural analysis of the homology model which provides elucidation of the effects of mutations, including a description of impacts of newly detected missense mutations.

Abstract 4229: Study on the germline mutation and protein expression of hMLH1 and hMSH2 gene in Chinese HNPCC probands.

Abstract BACKGROUND&amp;AIMS: Compare with sporadic colorectal cancer (SCRC), Hereditary nonpolyposis colorectal cancer (HNPCC) shows its own characteristcs associated with the molecular mechanism,clinical features,the methods for treatment and management of HNPCC kindreds. The molecular genetics basis of HNPCC was the mutation of mismatch repair (MMR) gene. Some HNPCC families which can found the mutation of MMR gene didn't fulfil any clinical criteria while more than fifty percent suspected HNPCC patients can't found mutation of MMR gene. Therefore, the tumorigenesis of HNPCC must be associated with other disease genes which have not been credited. The expression of hMLH1 and hMSH2 protein in 50 HNPCC probands fulfilling defferent clinical criteria and the germline mutation of hMLH1 and hMSH2 gene in 26 probands were analysed. Methods: The peripheral blood was collected from the probands of 26 HNPCC families fulfilling different clinical criterial, of which 7 families fulfilled AC, 19 kindreds fit BG. Genomic DNA was extracted following the manafacturer's protocol and used as the template to amplify 35 exons of the 2 genes by PCR. PCR products were purified and used as the template for direct DNA sequencing. The results of sequencing were analysed by different bioanalysis software. To further investigate the pathological effects of detected missense mutations, we analyse the same exon of hPMS2 gene using PCR-based sequencing in 130 healthy persons without family history. IHC envision two step method was performed.Results: 8 germline mutation of hMLH1 and hMSH2 was found in 26 HNPCC probands families. 4 fulfilled AC and 4 fulfilled BG..17 probands was found to be hMLH1 and hMSH2 protein deficient. Conclusion: The rate of germline mutation and protein expression was 30.8% and 34%. AC are the most sensitve clinical creteria to predict mutations. Immunohistochemical staining are reliable screening method with high predictive value for the detection of mutation. Some suspected HNPCC patients can't found mutation of MMR gene. Citation Format: Xia Sheng. Study on the germline mutation and protein expression of hMLH1 and hMSH2 gene in Chinese HNPCC probands. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4229. doi:10.1158/1538-7445.AM2013-4229

Multiplex mutation screening by mass spectrometry in gastrointestinal stromal tumours

Clinical decision making and optimal clinical trial design based on cancer genetic information will be increasingly informed by the mutational status of multiple genes. We performed mutation screening on 22 fresh frozen gastrointestinal stromal tumours (GISTs) using a multiplexed oncogene screening panel with a mass spectroscopy readout (MassARRAY). The panel can detect 390 known mutations across 30 genes, including several known to contribute to intracellular signalling in cancers (BRAF, PIK3CA, KRAS HRAS, NRAS, AKT1, CTNNB1, GNAQ, CDK4, MAP2K1 and MAP2K2). Direct Sanger sequencing confirmed that 16 cases (73%) harboured KIT mutations, affecting exon 11, 13 and 17, and the remaining six were wild-type for both KIT and PDGFRA. The sensitivity of the multiplexed oncogene screening panel was 100% for identifying missense mutations in KIT. Only 17% of the deletion mutations were detected, because the panel was not designed for detecting these. A substitution in FBX4 exon 1 (S8R), representing a germline single-nucleotide polymorphism, was observed in a case with KIT exon 11 missense mutation. No other mutations were identified, including in the six wild-type GISTs. Our results indicate that mutations other than KIT or PDGFRA are rare in GISTs. Although multiplex mutation screening by mass spectrometry detected missense mutations accurately, it is not sufficient to screen mutations because deletion mutations are common in GISTs.

Apparent mineralocorticoid excess syndrome: report of one family with three affected children

The syndrome of apparent mineralocorticoid excess (AME) is an autosomal recessive disorder characterized by hypertension, hypokalemia, low renin, and hypoaldosteronism. It is caused by deficiency of 11β-hydroxysteroid dehydrogenase, which results in a defect of the peripheral metabolism of cortisol to cortisone. As a consequence, the serum cortisol half-life (T½) is prolonged, ACTH is suppressed, and serum cortisol concentration is normal. The hormonal diagnosis of the disorder is made by the increased ratio of urine-free cortisol to cortisone. In patients with AME, this ratio is 5-18, while in normal individuals it is <0.5. These studies suggest that an abnormality in cortisol action or metabolism results in cortisol behaving as a potent mineralocorticoid and causing the syndrome of AME. We report three siblings - two female and one male - with the syndrome of apparent mineralocorticoid excess who presented with hypertension, hypokalemia, low renin, and low aldosterone levels. The finding of abnormally high ratios of 24-h urine-free cortisol to cortisone in our three patients (case 1, 8.4; case 2, 25; and case 3, 7.5) confirmed the diagnosis of apparent mineralocorticoid excess syndrome in these children. They were treated with oral potassium supplements. The addition of spironolactone resulted in a decrease in blood pressure, rise in serum potassium and a gradual increase in plasma renin activity in all three. In this study, the genetic testing of those three siblings with the typical clinical features of AME has detected missense mutation c.662C>T (p.Arg208Cys) in exon 3 of the HSD11B2 gene in the homozygous state.